npm - @ccp-nc/crystvis-js - Versions diffs - 0.7.0 → 0.7.2 - Mend

@ccp-nc/crystvis-js 0.7.0 → 0.7.2

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Files changed (44) hide show

package/lib/render.js +41 -15
package/package.json +3 -2
package/test/render.js +168 -0
package/test/setup-dom.cjs +65 -3
package/docs/data/search.json +0 -1
package/docs/fonts/Inconsolata-Regular.ttf +0 -0
package/docs/fonts/OpenSans-Regular.ttf +0 -0
package/docs/fonts/WorkSans-Bold.ttf +0 -0
package/docs/index.html +0 -59
package/docs/lib_model.module_js-AtomImage.html +0 -3
package/docs/lib_model.module_js-BondImage.html +0 -3
package/docs/lib_model.module_js-Model.html +0 -3
package/docs/lib_model.module_js.html +0 -3
package/docs/lib_modelview.module_js-ModelView.html +0 -12
package/docs/lib_modelview.module_js.html +0 -3
package/docs/lib_visualizer.module_js-CrystVis.html +0 -3
package/docs/lib_visualizer.module_js.html +0 -3
package/docs/model.js.html +0 -2191
package/docs/modelview.js.html +0 -473
package/docs/scripts/core.js +0 -726
package/docs/scripts/core.min.js +0 -23
package/docs/scripts/resize.js +0 -90
package/docs/scripts/search.js +0 -265
package/docs/scripts/search.min.js +0 -6
package/docs/scripts/third-party/Apache-License-2.0.txt +0 -202
package/docs/scripts/third-party/fuse.js +0 -9
package/docs/scripts/third-party/hljs-line-num-original.js +0 -369
package/docs/scripts/third-party/hljs-line-num.js +0 -1
package/docs/scripts/third-party/hljs-original.js +0 -5171
package/docs/scripts/third-party/hljs.js +0 -1
package/docs/scripts/third-party/popper.js +0 -5
package/docs/scripts/third-party/tippy.js +0 -1
package/docs/scripts/third-party/tocbot.js +0 -672
package/docs/scripts/third-party/tocbot.min.js +0 -1
package/docs/styles/clean-jsdoc-theme-base.css +0 -1159
package/docs/styles/clean-jsdoc-theme-dark.css +0 -412
package/docs/styles/clean-jsdoc-theme-light.css +0 -482
package/docs/styles/clean-jsdoc-theme-scrollbar.css +0 -30
package/docs/styles/clean-jsdoc-theme-without-scrollbar.min.css +0 -1
package/docs/styles/clean-jsdoc-theme.min.css +0 -1
package/docs/tutorial-Events.html +0 -13
package/docs/tutorial-Queries.html +0 -16
package/docs/tutorial-ThreejsMigration.html +0 -25
package/docs/visualizer.js.html +0 -810

package/docs/model.js.html DELETED Viewed

@@ -1,2191 +0,0 @@
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7h18v2H3v-2zm0 7h18v2H3v-2z"/></symbol></defs></svg></head><body data-theme="dark"><div class="sidebar-container"><div class="sidebar" id="sidebar"><div class="sidebar-items-container"><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-modules"><div>Modules</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js.html">lib/model.js</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js.html">lib/modelview.js</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-classes"><div>Classes</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div></div></div><div class="navbar-container" id="VuAckcnZhf"><nav class="navbar"><div class="navbar-left-items"></div><div class="navbar-right-items"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div><nav></nav></nav></div><div class="toc-container"><div class="toc-content"><span class="bold">On this page</span><div id="eed4d2a0bfd64539bb9df78095dec881"></div></div></div><div class="body-wrapper"><div class="main-content"><div class="main-wrapper"><section id="source-page" class="source-page"><header><h1 id="title" class="has-anchor">model.js</h1></header><article><pre class="prettyprint source lang-js"><code>'use strict';
-/**
- * @fileoverview Class holding the atomic models to be plotted
- * @module
- */
-import _ from 'lodash';
-import * as mjs from 'mathjs';
-import {
-    PeriodicTable as PeriodicTable
-} from 'mendeleev';
-import {
-    Atoms as Atoms
-} from '@ccp-nc/crystcif-parse';
-import * as utils from './utils.js';
-import * as data from './data.js';
-import {
-    QueryParser as QueryParser
-} from './query.js';
-import {
-    ModelView as ModelView
-} from './modelview.js';
-const LABEL_HEIGHT = 0.04; // For now fixed, just a value that works
-/** An 'image' of a single atom from a model. This represents a specific periodic copy of that atom (if applicable). */
-class AtomImage {
-    /**
-     * @class
-     * @param {Model} model     The model from which the image is from
-     * @param {int} index       Index of the atom in the model
-     * @param {Array} ijk       Indices of the cell in which the image is located
-     */
-    constructor(model, index, ijk) {
-        this._model = model;
-        this._index = index;
-        this._ijk = ijk || [0, 0, 0];
-        // String ID
-        this._id = this._index + '_' + _.join(this._ijk, '_');
-        // Integer index
-        this._img_index = utils.supercellIndex(index, this._ijk,
-            model.supercell, model.length);
-        this._xyz0 = model._positions[index];
-        this._bondsFrom = []; // BondImages of bonds for which this is atom1
-        this._bondsTo = []; // BondImages of bonds for which this is atom2
-        if (!model.periodic) {
-            this._fxyz0 = null;
-            this._fxyz = null;
-            this._xyz = this._xyz0;
-        } else {
-            this._fxyz0 = model._scaled_positions[index];
-            this._fxyz = [this._fxyz0[0] + ijk[0],
-                this._fxyz0[1] + ijk[1],
-                this._fxyz0[2] + ijk[2]
-            ];
-            this._xyz = mjs.multiply(this._fxyz, model._cell);
-        }
-        this._isotope = null; // By default look up the model
-        // Visual properties
-        this._visible = false;
-        this._color = this.cpkColor;
-        this._uses_cpk = true;
-        this._base_radius = this.vdwRadius / 4.0;
-        this._scale = 1.0;
-        this._opacity = 1.0;
-        this._highlighted = false;
-        this._mesh = null; // Will be created when first requested
-        this._aura = null;
-        this._labels = {};
-        this._ellipsoids = {};
-    }
-    /**
-     * Model this atom belongs to
-     * @readonly
-     * @type {Model}
-     */
-    get model() {
-        return this._model;
-    }
-    /**
-     * Renderer used by this atom
-     * @readonly
-     * @type {Renderer}
-     */
-    get renderer() {
-        var m = this.model;
-        if (m) {
-            return m._renderer;
-        }
-        return null;
-    }
-    /**
-     * Index of the atom
-     * @readonly
-     * @type {int}
-     */
-    get index() {
-        return this._index;
-    }
-    /**
-     * String ID of the image
-     * @readonly
-     * @type {String}
-     */
-    get id() {
-        return this._id;
-    }
-    /**
-     * Index of this image
-     * @readonly
-     * @type {int}
-     */
-    get imgIndex() {
-        return this._img_index;
-    }
-    /**
-     * Index of the species of this atom
-     * @readonly
-     * @type {int}
-     */
-    get speciesIndex() {
-        return this._model._species_indices[this._index];
-    }
-    /**
-     * Symbol of this atom's element
-     * @readonly
-     * @type {String}
-     */
-    get element() {
-        return this._model._elems[this._index];
-    }
-    /**
-     * Crystal site label of this atom
-     * @readonly
-     * @type {String}
-     */
-    get crystLabel() {
-        return this._model._labels[this._index];
-    }
-    /**
-     * Periodic table information for this atom's element
-     * @readonly
-     * @type {Object}
-     */
-    get elementData() {
-        return data.getElementData(this.element);
-    }
-    /**
-     * Information for this atom's isotope
-     * @readonly
-     * @type {Object}
-     */
-    get isotopeData() {
-        let idata = this._isotope;
-        if (idata === null)
-            idata = this._model._isotopes[this._index];
-        return idata;
-    }
-    /**
-     * Atomic mass of this atom's isotope
-     * @type {int}
-     */
-    get isotope() {
-        return this.isotopeData.A;
-    }
-    set isotope(A) {
-        this._isotope = data.getIsotopeData(this.element, A);
-        if (this._isotope === null)
-            throw Error('Isotope does not exist for this element');
-        // Reset color
-        if (this._uses_cpk) {
-            this.color = null;
-        }
-    }
-    /**
-     * Atomic mass of the global isotope set as default for this atom's species
-     * @type {int}
-     */
-    set isotopeGlobal(A) {
-        // Set the isotope for this atom in the model
-        let iso = data.getIsotopeData(this.element, A);
-        if (iso === null)
-            throw Error('Isotope does not exist for this element');
-        this._model._isotopes[this._index] = iso;
-        // Reset color
-        if (this._uses_cpk) {
-            this.color = null;
-        }
-    }
-    /**
-     * Atomic number of element
-     * @readonly
-     * @type {int}
-     */
-    get number() {
-        var el = PeriodicTable.getElement(this.element);
-        return (el ? el.number : 0);
-    }
-    /**
-     * Hex integer code of the conventional CPK color used for this element
-     * (altered in case of non-standard isotopes)
-     * @readonly
-     * @type {int}
-     */
-    get cpkColor() {
-        return data.getCpkColor(this.element, this.isotope);
-    }
-    /**
-     * Van dew Waals radius for this element
-     * @readonly
-     * @type {float}
-     */
-    get vdwRadius() {
-        return data.getVdwRadius(this.element);
-    }
-    /**
-     * Bonds from this atom
-     * @readonly
-     * @type {BondImage[]}
-     */
-    get bondsFrom() {
-        return Array.from(this._bondsFrom);
-    }
-    /**
-     * Bonds to this atom
-     * @readonly
-     * @type {BondImage[]}
-     */
-    get bondsTo() {
-        return Array.from(this._bondsTo);
-    }
-    /**
-     * All bonds connected to this atom
-     * @readonly
-     * @type {BondImage[]}
-     */
-    get bonds() {
-        return _.concat(this._bondsFrom, this._bondsTo);
-    }
-    /**
-     * All atoms bonded to this atom
-     * @readonly
-     * @type {AtomImage[]}
-     */
-    get bondedAtoms() {
-        return _.concat(_.map(this._bondsFrom, function(b) {
-                return b.atom2;
-            }),
-            _.map(this._bondsTo, function(b) {
-                return b.atom1;
-            }));
-    }
-    /**
-     * Cell indices of this atom image
-     * @readonly
-     * @type {int[]}
-     */
-    get ijk() {
-        return Array.from(this._ijk);
-    }
-    /**
-     * Position of this atom's original
-     * @readonly
-     * @type {float[]}
-     */
-    get xyz0() {
-        return Array.from(this._xyz0);
-    }
-    /**
-     * Position of this atom image
-     * @readonly
-     * @type {float[]}
-     */
-    get xyz() {
-        return Array.from(this._xyz);
-    }
-    /**
-     * Fractional coordinates of this atom's original
-     * @readonly
-     * @type {float[]}
-     */
-    get fxyz0() {
-        return Array.from(this._fxyz0);
-    }
-    /**
-     * Fractional coordinates of this atom image
-     * @readonly
-     * @type {float[]}
-     */
-    get fxyz() {
-        return Array.from(this._fxyz);
-    }
-    /**
-     * Index of the molecule this atom belongs to
-     * @readonly
-     * @type {int}
-     */
-    get moleculeIndex() {
-        return this._model._molinds[this._index];
-    }
-    /**
-     * Mesh corresponding to this atom image
-     * @readonly
-     * @type {AtomMesh}
-     */
-    get mesh() {
-        var r = this.renderer;
-        if (!this._mesh &amp;&amp; r) {
-            this._mesh = new r.Primitives.AtomMesh(this._xyz, this.radius, this._color);
-            this._mesh.image = this;
-        }
-        return this._mesh;
-    }
-    /**
-     * Aura used to highlight this atom image
-     * @readonly
-     * @type {AuraMesh}
-     */
-    get aura() {
-        var r = this.renderer;
-        if (!this._aura &amp;&amp; r) {
-            this._aura = new r.Primitives.AuraMesh({
-                radius: this.radius,
-                scale: 0.02
-            });
-            this.mesh.add(this._aura);
-        }
-        return this._aura;
-    }
-    // Get and set graphical properties
-    /**
-     * Whether the atom is visible
-     * @type {bool}
-     */
-    get visible() {
-        return this._visible;
-    }
-    set visible(v) {
-        this._visible = v;
-        var mesh = this.mesh;
-        if (v) {
-            this.renderer.add(mesh, 'model');
-        } else {
-            this.renderer.remove(mesh, 'model');
-        }
-        // Update aura visibility
-        this.highlighted = this._highlighted;
-        // Update connected bonds' visibility
-        for (let i = 0; i &lt; this._bondsFrom.length; ++i) {
-            let b = this._bondsFrom[i];
-            b.visible = b._visible;
-        }
-        for (let i = 0; i &lt; this._bondsTo.length; ++i) {
-            let b = this._bondsTo[i];
-            b.visible = b._visible;
-        }
-    }
-    /**
-     * Starting radius of the atom
-     * @type {float}
-     */
-    get baseRadius() {
-        return this._base_radius;
-    }
-    set baseRadius(r) {
-        if (r == null) { // Default value
-            r = this.vdwRadius / 4.0;
-        }
-        this._base_radius = r;
-        var mesh = this.mesh;
-        mesh.atom_radius = this.radius;
-    }
-    /**
-     * Scale of the atom
-     * @type {float}
-     */
-    get scale() {
-        return this._scale;
-    }
-    set scale(s) {
-        if (s == null) {
-            s = 1;
-        }
-        this._scale = s;
-        var mesh = this.mesh;
-        mesh.atom_radius = this.radius;
-    }
-    /**
-     * Final radius of the atom (starting radius * scale)
-     * @type {float}
-     */
-    get radius() {
-        return this._scale * this._base_radius;
-    }
-    set radius(r) {
-        if (r == null) {
-            r == this.baseRadius;
-        }
-        this.scale = r / this._base_radius;
-    }
-    /**
-     * Color of the atom
-     * @type {int}
-     */
-    get color() {
-        return this._color;
-    }
-    set color(c) {
-        if (c === null) {
-            c = this.cpkColor;
-            this._uses_cpk = true;
-        }
-        else {
-            this._uses_cpk = false;
-        }
-        this._color = c;
-        var mesh = this.mesh;
-        if (mesh) {
-            mesh.atom_color = c;
-        }
-        _.map(this._bondsFrom, function(b) {
-            b.color1 = c;
-        });
-        _.map(this._bondsTo, function(b) {
-            b.color2 = c;
-        });
-    }
-    /**
-     * Opacity of the atom
-     * @type {float}
-     */
-    get opacity() {
-        return this._opacity;
-    }
-    set opacity(o) {
-        if (o == null) {
-            o = 1;
-        }
-        this._opacity = o;
-        var mesh = this.mesh;
-        mesh.atom_opacity = o;
-        _.map(this._bondsFrom, function(b) {
-            b.opacity1 = o;
-        });
-        _.map(this._bondsTo, function(b) {
-            b.opacity2 = o;
-        });
-    }
-    /**
-     * Whether the atom is highlighted
-     * @type {bool}
-     */
-    get highlighted() {
-        return this._highlighted;
-    }
-    set highlighted(h) {
-        if (h == null) {
-            h = false;
-        }
-        this._highlighted = h;
-        var aura = this.aura;
-        if (h &amp;&amp; this._visible) {
-            aura.visible = true;
-        } else {
-            aura.visible = false;
-        }
-    }
-    /**
-     * Add a text label to the atom.
-     *
-     * @param {String}  text        Content of the label
-     * @param {String}  name        Name to use to refer to the label (necessary to overwrite/erase later)
-     * @param {Object}  parameters  Dictionary of other options (e.g. font family, text color, etc. See TextSprite)
-     */
-    addLabel(text, name, parameters = {}) {
-        this.removeLabel(name); // Precautionary
-        var defaults = {
-            faceCamera: true,
-            fixScale: true,
-            shift: [1.0*this.radius, 0, 0], // This just works well
-            height: LABEL_HEIGHT,
-        };
-        parameters = _.merge(defaults, parameters);
-        parameters.position = [0, 0, 0]; // This is not customizable
-        var r = this.renderer;
-        if (r) {
-            var label = new r.Primitives.TextSprite(text, parameters);
-            this._labels[name] = label;
-            this.mesh.add(label);
-        }
-    }
-    /**
-     * Remove the label of a given name
-     *
-     * @param {String}  name     Name of the label
-     */
-    removeLabel(name) {
-        let l = this._labels[name];
-        if (l)
-            this._mesh.remove(l);
-        delete this._labels[name];
-    }
-    /**
-     * Retrieve or set a label's properties
-     *
-     * @param {String}  name     Name of the label
-     * @param {String}  property Property to set
-     * @param {?}       value    Value to set. If omitted, returns the current
-     *                           value instead.
-     */
-    labelProperty(name, property, value = null) {
-        if (value) {
-            this._labels[name][property] = value;
-        } else {
-            return this._labels[name][property];
-        }
-    }
-    /**
-     * Add an ellipsoid to the atom.
-     *
-     * @param {TensorData | Object | Array}     data   The data to base the
-     *                                                 ellipsoid on. Can be:
-     *                                                 - a TensorData object;
-     *                                                 - an Object with 'eigenvalues'
-     *                                                   and 'eigenvectors' members
-     *                                                 - an Array of the form
-     *                                                 [eigenvalues, eigenvectors]
-     * @param {String}                          name   Name of the ellipsoid
-     * @param {Object}                          parameters Additional options to
-     *                                                     pass (see EllipsoidMesh)
-     */
-    addEllipsoid(data, name, parameters = {}) {
-        this.removeEllipsoid(name);
-        parameters = _.clone(parameters); // Avoid editing the reference object
-        if (data instanceof Array) {
-            parameters.eigenvalues = data[0];
-            parameters.eigenvectors = data[1];
-        } else {
-            parameters.eigenvalues = data.eigenvalues;
-            parameters.eigenvectors = data.eigenvectors;
-        }
-        if (parameters.ditherSeed == null) {
-            // As long as it's consistent for a given atom, the actual value is irrelevant
-            let seed = utils.hashCode(this._fxyz + name);
-            parameters.ditherSeed = seed/4294967295.0; // Reduce to ]0.5,-0.5]
-        }
-        var r = this.renderer;
-        if (r) {
-            var ellips = new r.Primitives.EllipsoidMesh(parameters);
-            this._ellipsoids[name] = ellips;
-            this.mesh.add(ellips);
-        }
-    }
-    /**
-     * Remove the ellipsoid with a given name
-     *
-     * @param {String}  name     Name of the ellipsoid
-     */
-    removeEllipsoid(name) {
-        let l = this._ellipsoids[name];
-        if (l)
-            this._mesh.remove(l);
-        delete this._ellipsoids[name];
-    }
-    /**
-     * Retrieve or set an ellipsoid's properties
-     *
-     * @param {String}  name     Name of the ellipsoid
-     * @param {String}  property Property to set
-     * @param {?}       value    Value to set. If omitted, returns the current
-     *                           value instead.
-     */
-    ellipsoidProperty(name, property, value = null) {
-        if (value) {
-            this._ellipsoids[name][property] = value;
-        } else {
-            return this._ellipsoids[name][property];
-        }
-    }
-    /**
-     * Get the value for one array for this image
-     * @param  {String} name    Name of the array
-     *
-     * @return {*}              Value of the array for this atom
-     */
-    getArrayValue(name) {
-        return this._model.getArray(name)[this._index];
-    }
-    // Check equality with another image
-    equals(ai) {
-        return (this._model == ai._model &amp;&amp;
-            this._index == ai._index &amp;&amp;
-            _.isEqual(this._ijk, ai._ijk));
-    }
-    // Return a copy, possibly shifted to a different cell
-    copy(shift = [0, 0, 0]) {
-        return new AtomImage(this._model,
-            this._index,
-            mjs.add(this._ijk, shift));
-    }
-}
-/** An 'image' of a single bond in the model. This represents the connection
-    between two specific AtomImages */
-class BondImage {
-    /**
-     * @class
-     * @param {Model}     model     The model from which the image is from
-     * @param {AtomImage} im1       AtomImage from which the bond starts
-     * @param {AtomImage} im2       AtomImage to which the bond ends
-     */
-    constructor(model, im1, im2) {
-        this._model = model;
-        this._im1 = im1;
-        this._im2 = im2;
-        this._im1._bondsFrom.push(this);
-        this._im2._bondsTo.push(this);
-        this._length = mjs.distance(this._im1.xyz, this._im2.xyz);
-        this._key = this._im1.imgIndex + '_' + this._im2.imgIndex;
-        // Visual properties
-        this._visible = true;
-        this._radius = 0.2;
-        this._opacity = 1.0;
-        this._mesh = null; // Created on first request
-    }
-    /**
-     * Model this bond belongs to
-     * @readonly
-     * @type {Model}
-     */
-    get model() {
-        return this._model;
-    }
-    /**
-     * Renderer used by this bond
-     * @readonly
-     * @type {Renderer}
-     */
-    get renderer() {
-        var m = this.model;
-        if (m) {
-            return m._renderer;
-        }
-        return null;
-    }
-    /**
-     * First atom connected to this bond
-     * @readonly
-     * @type {AtomImage}
-     */
-    get atom1() {
-        return this._im1;
-    }
-    /**
-     * Second atom connected to this bond
-     * @readonly
-     * @type {AtomImage}
-     */
-    get atom2() {
-        return this._im2;
-    }
-    /**
-     * A unique string key used to quickly reference the bond
-     * @readonly
-     * @type {String}
-     */
-    get key() {
-        // Used in dictionary for quick reference
-        return this._key;
-    }
-    /**
-     * Bond length in Angstroms
-     * @readonly
-     * @type {float}
-     */
-    get length() {
-        return this._length;
-    }
-    /**
-     * Mesh corresponding to this bond image
-     * @readonly
-     * @type {AtomMesh}
-     */
-    get mesh() {
-        var r = this.renderer;
-        if (!this._mesh &amp;&amp; r) {
-            this._mesh = new r.Primitives.BondMesh(this.atom1.xyz, this.atom2.xyz,
-                this._radius,
-                this.atom1.color, this.atom2.color);
-        }
-        return this._mesh;
-    }
-    /**
-     * Radius of the bond
-     * @type {float}
-     */
-    get radius() {
-        return this._radius;
-    }
-    set radius(r) {
-        if (r == null) {
-            r = 0.2;
-        }
-        this._radius = r;
-        var mesh = this.mesh;
-        if (mesh) {
-            mesh.bond_radius = r;
-        }
-    }
-    /**
-     * First color of the bond
-     * @type {int}
-     */
-    set color1(c) {
-        if (c == null) {
-            c = this._im1.color;
-        }
-        var mesh = this.mesh;
-        if (mesh) {
-            mesh.bond_color_1 = c;
-        }
-    }
-    /**
-     * Second color of the bond
-     * @type {int}
-     */
-    set color2(c) {
-        if (c == null) {
-            c = this._im2.color;
-        }
-        var mesh = this.mesh;
-        if (mesh) {
-            mesh.bond_color_2 = c;
-        }
-    }
-    /**
-     * First opacity of the bond
-     * @type {float}
-     */
-    set opacity1(o) {
-        if (o == null) {
-            o = this._im1.opacity;
-        }
-        var mesh = this.mesh;
-        if (mesh) {
-            mesh.bond_opacity_1 = o;
-        }
-    }
-    /**
-     * Second opacity of the bond
-     * @type {float}
-     */
-    set opacity2(o) {
-        if (o == null) {
-            o = this._im2.opacity;
-        }
-        var mesh = this.mesh;
-        if (mesh) {
-            mesh.bond_opacity_2 = o;
-        }
-    }
-    /**
-     * Whether the bond is visible
-     * @type {bool}
-     */
-    get visible() {
-        return this._visible;
-    }
-    set visible(v) {
-        this._visible = v;
-        v = v &amp;&amp; this.atom1.visible &amp;&amp; this.atom2.visible;
-        var mesh = this.mesh;
-        if (v) {
-            this.renderer.add(mesh, 'model');
-        } else {
-            this.renderer.remove(mesh, 'model');
-        }
-    }
-}
-class Model {
-    /**
-     * An object containing an Atomic structure and taking care of its periodic
-     * nature, allowing querying and selection, and so on.
-     * @class
-     * @param {crystcif.Atoms}  atoms       Atomic structure, in crystcif's Atoms format
-     * @param {Object}          parameters  Additional options:
-     *
-     * - `supercell`
-     * - `molecularCrystal` (if true, load full molecules in central unit cell)
-     * - `useNMRActiveIsotopes` (if true, all isotopes are set by default to the most common
-     *                                        one with non-zero spin)
-     * - `vdwScaling` (scale van der Waals radii by a constant factor)
-     * - `vdwElementScaling` (table of per-element factors to scale VdW radii by)
-     */
-    constructor(atoms, parameters = {}) {
-        var defaults = {
-            supercell: [1, 1, 1],
-            molecularCrystal: false,
-            useNMRActiveIsotopes: false,
-            vdwScaling: 1.0,
-            vdwElementScaling: {}
-        };
-        parameters = _.merge(defaults, parameters);
-        this._vdwScaling = parameters.vdwScaling;
-        this._vdwElementScaling = parameters.vdwElementScaling;
-        const initMolecules = ((atoms, supercell) => {
-            if (!(atoms instanceof Atoms)) {
-                throw new Error('Model must be initialised with a loaded Atoms object');
-            }
-            this._atoms_base = atoms;
-            this._data = {};
-            /* Load the positions, cell, and other key data
-               Important: to save memory, we're simply storing references.
-               These are NOT to be changed!
-            */
-            this._elems = this._atoms_base._arrays['symbols'];
-            this._isotopes = this._elems.map((el) => {
-                const iso = parameters.useNMRActiveIsotopes? 'nmr' : null;
-                let isodata = data.getIsotopeData(el, iso);
-                if (isodata === null) {
-                    // No NMR active isotope?
-                    isodata = data.getIsotopeData(el);
-                }
-                return isodata;
-            });
-            this._nums = this._atoms_base._arrays['numbers'];
-            this._positions = this._atoms_base._arrays['positions'];
-            this._cell = this._atoms_base._cell;
-            this._pbc = this._atoms_base._pbc;
-            this._periodic = !this._pbc.includes(false);
-            this._inv_cell = this._atoms_base._inv_cell;
-            this._supercell = [1, 1, 1];
-            this._supercell_grid = [
-                [0, 0, 0]
-            ];
-            // Species indices (used for labels)
-            let sp_count = {};
-            this._species_indices = [];
-            this._species_indices = this._elems.map((s, i) => {
-                let c = sp_count[s];
-                c = c? c : 0;
-                sp_count[s] = c+1;
-                return c;
-            });
-            let has_cif_labels = false;
-            // Crystallographic labels
-            if ('labels' in this._atoms_base._arrays) {
-                // If any of the labels don't match the element,
-                // then we're assuming they're crystallographic (CIF-style) labels
-                if (this._atoms_base._arrays['labels'].some((l, i) => {
-                    return l !== this._elems[i];
-                })) {
-                    // then use them
-                    has_cif_labels = true;
-                    this._labels = this._atoms_base._arrays['labels'];
-                } else {
-                    // otherwise, build new ones and
-                    // throw a warning to user syaing we're doing this
-                    this._labels = [];
-                    for (let i = 0; i &lt; this._elems.length; ++i) {
-                        this._labels.push(this._elems[i] + '_' + (this._species_indices[i]+1));
-                    }
-                    console.warn('No crystallographic labels found in CIF file. Building new ones.');
-                }
-            }
-            else {
-                // Build them
-                this._labels = [];
-                for (let i = 0; i &lt; this._elems.length; ++i) {
-                    this._labels.push(this._elems[i] + '_' + (this._species_indices[i]+1));
-                }
-            }
-            this._has_cif_labels = has_cif_labels; // defaults to false
-            // Cryst label indices
-            let lab_count = {};
-            this._label_indices = [];
-            this._label_indices = this._labels.map((s, i) => {
-                let c = lab_count[s];
-                c = c? c : 0;
-                lab_count[s] = c+1;
-                return c;
-            });
-            if (this._periodic) {
-                // R matrix: indispensable for calculations of periodic distances
-                this._r_matrix = mjs.multiply(this._cell, mjs.transpose(this._cell));
-                var ediag = mjs.eigs(this._r_matrix);
-                // Sort by eigenvalue
-                var evecs = ediag.eigenvectors.map(e => e.vector);
-                ediag = _.zip(ediag.values, evecs);
-                ediag = _.sortBy(ediag, function(x) {
-                    return x[0];
-                });
-                ediag = _.unzip(ediag);
-                this._r_diag = {
-                    values: ediag[0],
-                    vectors: ediag[1],
-                };
-                this._supercell = supercell; // Default
-                this._supercell_grid = utils.supercellGrid(supercell);
-                this._scaled_positions = this._atoms_base.get_scaled_positions();
-            }
-            // Compile all images for this supercell
-            this._atom_images = this._atomImages();
-            this._computeBonds();
-            this._computeMolecules();
-        }).bind(this);
-        initMolecules(atoms, parameters.supercell);
-        // if parameters.molecularCrystal, is null, we need to check if the atoms
-        // contains organic molecules -- i.e. if there is at least one  C-H bond
-        if (parameters.molecularCrystal || (parameters.molecularCrystal === null &amp;&amp;
-            this._queryCHBond())) {
-            this._molecularCrystal = true;
-            atoms = _.cloneDeep(atoms);
-            var pos = this.positions;
-            for (let i = 0; i &lt; this.length; ++i) {
-                let mol_i = this._molinds[i];
-                let mol = this._molecules[mol_i];
-                for (let j = 0; j &lt; mol.length; ++j) {
-                    var a = mol[j];
-                    if (a.index == i) {
-                        pos[i] = mjs.add(pos[i], this.fracToAbs(a.cell));
-                    }
-                }
-            }
-            atoms.set_array('positions', pos);
-            initMolecules(atoms, parameters.supercell);
-        }
-        this._primitives = {}; // Any additional primitives drawn on this model
-        this._bond_images = this._bondImages();
-        // A special ModelView for convenience
-        this._all = new ModelView(this, _.range(this._atom_images.length));
-        // Parser for queries
-        this._qparse = new QueryParser({
-            'all': this._queryAll,
-            'indices': this._queryIndices,
-            'elements': this._queryElements,
-            'cell': this._queryCell,
-            'box': this._queryBox,
-            'sphere': this._querySphere,
-            'bonded': this._queryBonded,
-            'molecule': this._queryMolecule,
-        }, this);
-        // By default no rendering
-        this.renderer = null;
-    }
-    // Using the .get_ methods of _atoms guarantees these are copies,
-    // not pointers to the real thing
-    /**
-     * Number of atoms in this model's original cell
-     * @readonly
-     * @type {int}
-     */
-    get length() {
-        return this._atoms_base.length();
-    }
-    /**
-     * Chemical symbols in this model's original cell
-     * @readonly
-     * @type {String[]}
-     */
-    get symbols() {
-        return this._atoms_base.get_chemical_symbols();
-    }
-    /**
-     * Atomic numbers in this model's original cell
-     * @readonly
-     * @type {int[]}
-     */
-    get numbers() {
-        return this._atoms_base.get_atomic_numbers();
-    }
-    /**
-     * Coordinates of the atoms in this model's original cell
-     * @readonly
-     * @type {Array[]}
-     */
-    get positions() {
-        return this._atoms_base.get_positions();
-    }
-    /**
-     * Fractional coordinates of the atoms in this model's original cell
-     * @readonly
-     * @type {Array[]}
-     */
-    get scaledPositions() {
-        return this._atoms_base.get_scaled_positions();
-    }
-    /**
-     * Unit cell of the model's original cell
-     * @readonly
-     * @type {Array[]}
-     */
-    get cell() {
-        return this._atoms_base.get_cell();
-    }
-    /**
-     * Periodic boundary conditions
-     * @readonly
-     * @type {bool[]}
-     */
-    get pbc() {
-        return this._atoms_base.get_pbc();
-    }
-    /**
-     * Additional information from the model's original cell
-     * @readonly
-     * @type {Object}
-     */
-    get info() {
-        return this._atoms_base.info;
-    }
-    /**
-     * Whether this model is periodic in all three directions of space
-     * @readonly
-     * @type {bool}
-     */
-    get periodic() {
-        return this._periodic;
-    }
-    /**
-     * Indices of each atom by their species (e.g. C1, C2, H1, C3, H2, etc.)
-     * @readonly
-     * @type {int[]}
-     */
-    get speciesIndices() {
-        return Array.from(this._species_indices);
-    }
-    /**
-     * Crystallographic labels of each atom
-     * @readonly
-     * @type {String[]}
-     */
-    get crystalLabels() {
-        return Array.from(this._labels);
-    }
-    /**
-     * Shape of the supercell for this model
-     * @readonly
-     * @type {int[]}
-     */
-    get supercell() {
-        return Array.from(this._supercell);
-    }
-    /**
-     * Full grid of origin coordinates of the cells making up the supercell
-     * @readonly
-     * @type {Array[]}
-     */
-    get supercellGrid() {
-        return JSON.parse(JSON.stringify(this._supercell_grid));
-    }
-    /**
-     * Atom images in this model
-     * @readonly
-     * @type {AtomImage[]}
-     */
-    get atoms() {
-        return Array.from(this._atom_images);
-    }
-    /**
-     * ModelView containing all the atoms of the image
-     * @readonly
-     * @type {ModelView}
-     */
-    get all() {
-        return this._all;
-    }
-    /**
-     * Graphical object representing the unit cell's axes
-     * @readonly
-     * @type {AxesMesh}
-     */
-    get axes() {
-        return this._cartesian_axes;
-    }
-    /**
-     * Graphical object representing the unit cell's box
-     * @readonly
-     * @type {BoxMesh}
-     */
-    get box() {
-        return this._cartesian_box;
-    }
-    /**
-     * Global scaling factor for Van der Waals radii
-     * @readonly
-     * @type {float}
-     */
-    get vdwScaling() {
-        return this._vdwScaling;
-    }
-    /**
-     * Table of scaling factors by element for Van der Waals radii
-     * @readonly
-     * @type {Object}
-     */
-    get vdwElementScaling() {
-        return JSON.parse(JSON.stringify(this._vdwElementScaling));
-    }
-    /**
-     * Renderer used for this model's graphics
-     * @type {Renderer}
-     */
-    set renderer(r) {
-        if (r) {
-            this._renderer = r;
-            if (this.periodic) {
-                // Create axes and box
-                if (!this._cartesian_box) {
-                    this._cartesian_box = new r.Primitives.BoxMesh(this.cell, {color:r.theme.cell_line_color});
-                }
-                if (!this._cartesian_axes) {
-                    this._cartesian_axes = new r.Primitives.AxesMesh(this.cell, {
-                        linewidth: 1.5
-                    });
-                }
-                r.add(this._cartesian_box);
-                r.add(this._cartesian_axes);
-            }
-            // And the primitives
-            for (var name in this._primitives) {
-                var p = this._primitives[name];
-                r.add(p);
-            }
-        } else {
-            if (this._renderer)
-                this._renderer.clear();
-            this._renderer = null;
-        }
-    }
-    // Set and get arrays on the underlying Atoms object
-    /**
-     * Set an array for the underlying Atoms object
-     * @param {String}  name Name of the array to use
-     * @param {Array}   arr  Array to store
-     */
-    setArray(name, arr) {
-        this._atoms_base.set_array(name, arr);
-    }
-    /**
-     * Retrieve an array from the underlying Atoms object
-     * @param   {String}    name    Name of the array to retrieve
-     * @return  {Array}             Retrieved array
-     */
-    getArray(name) {
-        return this._atoms_base.get_array(name);
-    }
-    /**
-     * Check if an array exists in the underlying Atoms object
-     * @param   {String}    name    Name of the array to check
-     * @return  {bool}              Whether the array exists
-     */
-    hasArray(name) {
-        return (name in this._atoms_base._arrays);
-    }
-    /**
-     * Delete an array from the underlying Atoms object
-     * @param   {String}    name    Name of the array to delete
-     */
-    deleteArray(name) {
-        delete this._atoms_base._arrays[name];
-    }
-    // These functions are for adding and removing graphical representations
-    // that are meant to be drawn on to of the existing 3D model
-    /**
-     * Add link drawn on model
-     *
-     * @param {Atom | Array} from       Starting point
-     * @param {Atom | Array} to         End point
-     * @param {String} name             Name to use for the link object
-     * @param {String} label            Text label to add to the link
-     * @param {Object} parameters       Additional parameters (see LineMesh)
-     */
-    addLink(from, to, name = 'link', label = null, parameters = {}) {
-        this.removeGraphics(name);
-        parameters = _.clone(parameters); // Avoid editing the reference object
-        var r = this._renderer;
-        if (r) {
-            var link = new r.Primitives.LineMesh(from, to, parameters);
-            this._primitives[name] = link;
-            r.add(link);
-            if (label) {
-                var text = new r.Primitives.TextSprite(label, {
-                    color: parameters.color,
-                    fixScale: true,
-                    faceCamera: true,
-                    height: parameters.height || LABEL_HEIGHT,
-                    shift: [LABEL_HEIGHT, 0, 0],
-                    onOverlay: parameters.onOverlay
-                });
-                link.add(text);
-            }
-        }
-    }
-    /**
-     * Add a sphere drawn on model
-     *
-     * @param {Atom | Array}    center      Center of the sphere
-     * @param {float}           radius      Radius of the sphere
-     * @param {String}          name        Name to use for the sphere object
-     * @param {Object}          parameters  Additional parameters (see EllipsoidMesh)
-     */
-    addSphere(center, radius, name='sphere', parameters = {}) {
-        this.removeGraphics(name);
-        var r = this._renderer;
-        if (r) {
-            parameters = _.merge({
-                color: 0xffffff,
-                opacity: 0.5,
-                opacityMode: r.Primitives.EllipsoidMesh.DITHER,
-                showCircles: true,
-                showAxes: true
-            }, parameters); // Avoid editing the reference object
-            var sph = new r.Primitives.EllipsoidMesh({
-                color: parameters.color,
-                opacity: parameters.opacity,
-                opacityMode: parameters.opacityMode,
-                showCircles: parameters.showCircles,
-                showAxes: parameters.showAxes,
-                scalingFactor: radius,
-                center: center
-            });
-            this._primitives[name] = sph;
-            r.add(sph);
-        }
-    }
-    /**
-     * Remove the graphical object with a given name
-     *
-     * @param {String}  name     Name of the graphical object to remove
-     */
-    removeGraphics(name) {
-        var g = this._primitives[name];
-        var r = this._renderer;
-        if (g &amp;&amp; r)
-            r.remove(g);
-        delete this._primitives[name];
-    }
-    /**
-     * Remove all graphical objects
-     */
-    clearGraphics() {
-        var r = this._renderer;
-        if (r) {
-            _.map(this._primitives, function(g) {
-                r.remove(g);
-            });
-        }
-        this._primitives = {};
-    }
-    /**
-     * Compute the bonds within the model. For internal use
-     * @private
-     */
-    _computeBonds() {
-        var N = this.length;
-        this._bondmat = Array(N); // Bond matrix
-        this._bondmat = _.map(this._bondmat, function() {
-            return _.map(Array(N), function() {
-                return [];
-            });
-        });
-        // Van der Waals radii by element
-        var vdwf = this._vdwScaling;
-        var vdwf_table = this._vdwElementScaling;
-        var vdwr = _.map(this.symbols, function(s) {
-            var f = vdwf;
-            if (s in vdwf_table) {
-                f = vdwf_table[s];
-            }
-            return data.getVdwRadius(s)*f;
-        });
-        var maxr = _.max(vdwr);
-        var cell = this.cell;
-        var sgrid = [
-            [0, 0, 0]
-        ];
-        var p = this._positions;
-        if (this._periodic) {
-            var scell = this.minimumSupercell(maxr);
-            sgrid = utils.supercellGrid(scell);
-        }
-        // Now iterate over all atom pairs
-        for (let i = 0; i &lt; this.length; ++i) {
-            var p1 = p[i];
-            for (let j = i; j &lt; this.length; ++j) {
-                var p2 = p[j];
-                for (let k = 0; k &lt; sgrid.length; ++k) {
-                    var c = sgrid[k];
-                    if ((i == j) &amp;&amp; (c[0] == 0 &amp;&amp; c[1] == 0 &amp;&amp; c[2] == 0)) {
-                        // Just the same atom, skip
-                        continue;
-                    }
-                    var r = [0, 0, 0];
-                    // Here we write the algebra explicitly
-                    // for efficiency reasons
-                    if (this._periodic) {
-                        r[0] = c[0] * cell[0][0] + c[1] * cell[1][0] + c[2] * cell[2][0];
-                        r[1] = c[0] * cell[0][1] + c[1] * cell[1][1] + c[2] * cell[2][1];
-                        r[2] = c[0] * cell[0][2] + c[1] * cell[1][2] + c[2] * cell[2][2];
-                    }
-                    r = [p2[0] - p1[0] + r[0], p2[1] - p1[1] + r[1], p2[2] - p1[2] + r[2]];
-                    r = Math.sqrt(r[0] * r[0] + r[1] * r[1] + r[2] * r[2]);
-                    if (r &lt; (vdwr[i] + vdwr[j]) / 2.0) {
-                        // Bond!
-                        this._bondmat[i][j].push([c[0], c[1], c[2]]);
-                        this._bondmat[j][i].push([-c[0], -c[1], -c[2]]);
-                    }
-                }
-            }
-        }
-    }
-    /**
-     * Check if any C-H bonds are present
-     * @return {bool} Whether any C-H bonds are present
-     * @private
-     */
-    _queryCHBond() {
-        // make sure bondmat is present
-        if (!this._bondmat) {
-            this._computeBonds();
-        }
-        var symbols = this._atoms_base.get_chemical_symbols();
-        var bondmat = this._bondmat;
-        var n = symbols.length;
-        for (var i = 0; i &lt; n; i++) {
-            var bonds = bondmat[i];
-            var a = symbols[i];
-            if (a == 'C') {
-                // loop over bonds and check if any are H
-                for (var j = 0; j &lt; n; j++) {
-                    // if bonds[j] is not an empty array
-                    if (bonds[j].length) {
-                        if (symbols[j] == 'H') {
-                            return true;
-                        }
-                    }
-                }
-            }
-        }
-        return false;
-    }
-    /**
-     * Compute the molecules within the model. For internal use
-     * @private
-     */
-    _computeMolecules() {
-        this._molecules = [];
-        this._molinds = [];
-        if (this.length &lt; 2) {
-            // No molecules can be computed
-            this._molecules = null;
-            return;
-        }
-        var mol_sets = [];
-        var unsorted_atoms = _.range(this.length);
-        while (unsorted_atoms.length > 0) {
-            var mol_queue = [
-                [unsorted_atoms.shift(), [0, 0, 0]]
-            ];
-            var current_mol = [];
-            var current_mol_cells = [];
-            while (mol_queue.length > 0) {
-                var ac1 = mol_queue.shift();
-                var a1 = ac1[0];
-                var c1 = ac1[1];
-                current_mol.push(a1);
-                current_mol_cells.push(c1);
-                // Find linked atoms
-                var link1 = this._bondmat[a1];
-                for (let i in link1) {
-                    var a2 = parseInt(i);
-                    var link12 = link1[i];
-                    // Is a2 still unsorted?
-                    if (!unsorted_atoms.includes(a2) || link12.length == 0)
-                        continue;
-                    for (let j = 0; j &lt; link12.length; ++j) {
-                        var c2 = link12[j];
-                        mol_queue.push([a2, mjs.add(c1, c2)]);
-                    }
-                    unsorted_atoms.splice(unsorted_atoms.indexOf(a2), 1);
-                }
-            }
-            mol_sets.push([
-                current_mol,
-                current_mol_cells
-            ]);
-        }
-        for (let i = 0; i &lt; mol_sets.length; ++i) {
-            var mol = [];
-            for (let j = 0; j &lt; mol_sets[i][0].length; ++j) {
-                mol.push({
-                    'index': mol_sets[i][0][j],
-                    'cell': mol_sets[i][1][j]
-                });
-            }
-            this._molecules.push(mol);
-        }
-        // Assign the molecule's index for each atom
-        this._molinds = _.range(this.length);
-        for (let i = 0; i &lt; this._molecules.length; ++i) {
-            var m = this._molecules[i];
-            for (let j = 0; j &lt; m.length; ++j) {
-                var a = m[j];
-                this._molinds[a.index] = i;
-            }
-        }
-    }
-    /**
-     * Return a list of all AtomImages within the given supercell.
-     *
-     * @private
-     * @return {AtomImage[]}  List of AtomImage objects
-     */
-    _atomImages() {
-        var sgrid = this._supercell_grid;
-        var imgs = [];
-        var indices = _.range(this.length);
-        var model = this;
-        for (let i = 0; i &lt; sgrid.length; ++i) {
-            var cell = sgrid[i];
-            imgs = imgs.concat(_.map(indices, function(a) {
-                return new AtomImage(model, a, cell);
-            }));
-        }
-        return imgs;
-    }
-    /**
-     * Return a list of all BondImages within the given supercell.
-     *
-     * @private
-     * @return {BondImage[]}  List of BondImage objects
-     */
-    _bondImages() {
-        var bondimgs = [];
-        for (let ii = 0; ii &lt; this._atom_images.length; ++ii) {
-            var im1 = this._atom_images[ii];
-            var i = im1.index;
-            var bonds = this._bondmat[i];
-            var c1 = im1.ijk;
-            for (let j = i; j &lt; this.length; ++j) {
-                var blist = bonds[j];
-                for (let k = 0; k &lt; blist.length; ++k) {
-                    var r = blist[k];
-                    var c2 = [c1[0] + r[0], c1[1] + r[1], c1[2] + r[2]];
-                    var jj = utils.supercellIndex(j, c2, this._supercell, this.length);
-                    if (jj >= 0 &amp;&amp; jj &lt; this._atom_images.length) {
-                        var im2 = this._atom_images[jj];
-                        var bimg = new BondImage(this, im1, im2);
-                        bondimgs.push(bimg);
-                    }
-                }
-            }
-        }
-        return bondimgs;
-    }
-    /**
-     * Convert fractional coordinates to absolute
-     *
-     * @param  {float[]} fx Fractional coordinates
-     * @return {float[]}    Absolute coordinates
-     */
-    fracToAbs(fx) {
-        if (!this.periodic) {
-            return null
-        }
-        var c = this._atoms_base._cell;
-        return [fx[0] * c[0][0] + fx[1] * c[1][0] + fx[2] * c[2][0],
-            fx[0] * c[0][1] + fx[1] * c[1][1] + fx[2] * c[2][1],
-            fx[0] * c[0][2] + fx[1] * c[1][2] + fx[2] * c[2][2]
-        ];
-    }
-    /**
-     * Convert absolute coordinates to fractional
-     *
-     * @param  {float[]} x  Absolute coordinates
-     * @return {float[]}    Fractional coordinates
-     */
-    absToFrac(x) {
-        if (!this.periodic) {
-            return null
-        }
-        var ic = this._atoms_base._inv_cell;
-        return [x[0] * ic[0][0] + x[1] * ic[1][0] + x[2] * ic[2][0],
-            x[0] * ic[0][1] + x[1] * ic[1][1] + x[2] * ic[2][1],
-            x[0] * ic[0][2] + x[1] * ic[1][2] + x[2] * ic[2][2]
-        ];
-    }
-    /**
-     * Compute and return the minimum supercell that guarantees
-     * containing all atoms at a maximum distance r from those in the
-     * [0,0,0] cell.
-     *
-     * @param {float}   r       Maximum distance that must be contained within the supercell
-     */
-    minimumSupercell(r) {
-        var diag = _.map(this._r_diag.values, function(x) {
-            return mjs.pow(x, -0.5)
-        });
-        var utransf_mat = mjs.multiply(this._r_diag.vectors, mjs.diag(diag));
-        var utransf_norm = mjs.transpose(utransf_mat);
-        for (let i = 0; i &lt; 3; ++i) {
-            var norm = mjs.norm(utransf_mat[i]);
-            for (let j = 0; j &lt; 3; ++j) {
-                utransf_norm[j][i] *= r / norm;
-            }
-        }
-        var qmatrix = mjs.multiply(utransf_mat, utransf_norm);
-        var scell = [];
-        for (let i = 0; i &lt; 3; ++i) {
-            var b = 0;
-            for (let j = 0; j &lt; 3; ++j) {
-                b = Math.max(Math.ceil(Math.abs(qmatrix[i][j])), b);
-            }
-            scell.push(2 * b + 1);
-        }
-        return scell;
-    }
-    /**
-     * Find a group of atoms based on a given query and return as AtomImages
-     * @param  {Array} query  A search query for atoms. Must use nested lists
-     *                        of types and arguments, and can use logic
-     *                        operators $and, $or and $xor.
-     * @return {ModelView}    ModelView object for found atoms
-     */
-    find(query) {
-        var found = this._qparse.parse(query);
-        return this.view(found);
-    }
-    /** Create a new ModelView for this model, using a given list of indices
-     *  @param {Array} indices Indices of atoms to include in the ModelView
-     *
-     *  @return {ModelView}   ModelView object for specified indices
-     */
-    view(indices) {
-        return new ModelView(this, indices);
-    }
-    /**
-     * Reconstruct a {@link ModelView} from a plain array of atom-image indices,
-     * as produced by {@link ModelView#toIndices}.  This is the stable public API
-     * for deserialising a saved selection.
-     *
-     * @param  {number[]} indices
-     * @return {ModelView}
-     */
-    viewFromIndices(indices = []) {
-        return this.view(indices);
-    }
-    /**
-     * Reconstruct a {@link ModelView} from an array of crystallographic site
-     * labels (`crystLabel`), as produced by {@link ModelView#toLabels}.  This
-     * is resilient to atom-index reordering across reloads.
-     *
-     * @param  {string[]} labels
-     * @return {ModelView}
-     */
-    viewFromLabels(labels = []) {
-        const wanted = new Set(labels);
-        const indices = [];
-        for (let i = 0; i &lt; this._atom_images.length; ++i) {
-            if (wanted.has(this._atom_images[i].crystLabel)) {
-                indices.push(i);
-            }
-        }
-        return this.view(indices);
-    }
-    /**
-     * Set a property on a series of atom images
-     *
-     * @private
-     * @param {AtomImage[]} aimages     List of AtomImages, or their indices
-     * @param {String}      name        Name of the property to set
-     * @param {String}      value       Value to set to the property
-     */
-    _setAtomsProperty(aimages, name, value) {
-        // Value can be a single value or an Array
-        var isarr = (value instanceof Array);
-        for (let i = 0; i &lt; aimages.length; ++i) {
-            var id = aimages[i];
-            if (id instanceof AtomImage)
-                id = id.imgIndex;
-            this._atom_images[id][name] = isarr ? value[i] : value;
-        }
-    }
-    /**
-     * Set a property on a series of bond images
-     *
-     * @private
-     * @param {BondImage[]} aimages     List of BondImages
-     * @param {String}      name        Name of the property to set
-     * @param {String}      value       Value to set to the property
-     */
-    _setBondsProperty(bimages, name, value) {
-        // Value can be a single value or an Array
-        var isarr = (value instanceof Array);
-        for (let i = 0; i &lt; bimages.length; ++i) {
-            var bimg = bimages[i];
-            bimg[name] = isarr ? value[i] : value;
-        }
-    }
-    // Query functions. These are for internal use. They return the indices of
-    // AtomImages in the _atom_images array.
-    /**
-     * @private
-     */
-    _queryAll() {
-        // All atoms
-        return _.range(this._atom_images.length);
-    }
-    /**
-     * @private
-     */
-    _queryIndices(indices) {
-        if (typeof(indices) == 'number') {
-            indices = [indices]; // A single index
-        }
-        var scell = this.supercell;
-        var n = this.length;
-        var scgrid = this._supercell_grid;
-        var found = _.map(indices, function(i) {
-            return _.map(scgrid, function(ijk) {
-                return utils.supercellIndex(i, ijk, scell, n);
-            });
-        });
-        return _.flatten(found);
-    }
-    /**
-     * @private
-     */
-    _queryElements(elems) {
-        if (_.isString(elems)) {
-            elems = [elems]; // A single symbol
-        }
-        var indices = _.reduce(this._elems, function(inds, s, i) {
-            if (elems.indexOf(s) > -1) {
-                inds.push(i);
-            }
-            return inds;
-        }, []);
-        return this._queryIndices(indices);
-    }
-   /**
-     * @private
-     */
-    _queryLabels(labels) {
-        if (_.isString(labels)) {
-            labels = [labels]; // A single label
-        }
-        var indices = _.reduce(this._labels, function(inds, s, i) {
-            if (labels.indexOf(s) > -1) {
-                inds.push(i);
-            }
-            return inds;
-        }, []);
-        return this._queryIndices(indices);
-    }
-    /**
-     * @private
-     */
-    _queryCell(ijk) {
-        // Check if ijk is contained in the supercell's limits
-        var ind = _.findIndex(this._supercell_grid, function(x) {
-            return _.isEqual(x, ijk);
-        });
-        if (ind &lt; 0) {
-            return [];
-        }
-        var scell = this.supercell;
-        var n = this.length;
-        var found = _.map(_.range(n), function(x) {
-            return utils.supercellIndex(x, ijk, scell, n);
-        });
-        return found;
-    }
-    /**
-     * @private
-     */
-    _queryBox(x0, x1) {
-        if (x0 instanceof AtomImage) {
-            x0 = x0.xyz;
-        }
-        if (x1 instanceof AtomImage) {
-            x1 = x1.xyz;
-        }
-        // Box sides?
-        var box = _.zip(x0, x1);
-        var xmin = _.map(box, _.min);
-        var xmax = _.map(box, _.max);
-        var fxmin;
-        var fxmax;
-        if (this.periodic) {
-            var fx0 = this.absToFrac(x0);
-            var fx1 = this.absToFrac(x1);
-            var fbox = _.zip(fx0, fx1);
-            fxmin = _.map(fbox, _.min);
-            fxmax = _.map(fbox, _.max);
-            fxmin = _.map(fxmin, Math.floor);
-            fxmax = _.map(fxmax, Math.ceil);
-            // Now add supercell limits
-            var scmin = this._supercell_grid[0];
-            var scmax = this._supercell_grid[this._supercell_grid.length - 1];
-            fxmin = _.zipWith(fxmin, scmin, function(f, s) {
-                return Math.max(f, s);
-            });
-            fxmax = _.zipWith(fxmax, scmax, function(f, s) {
-                return Math.min(f, s + 1);
-            });
-        } else {
-            fxmin = [0, 0, 0];
-            fxmax = [1, 1, 1];
-        }
-        var found = []
-        // Now iterate over the cells, and atoms
-        for (let i = fxmin[0]; i &lt; fxmax[0]; ++i) {
-            for (let j = fxmin[1]; j &lt; fxmax[1]; ++j) {
-                for (let k = fxmin[2]; k &lt; fxmax[2]; ++k) {
-                    // var p0 = this.fracToAbs([i, j, k]);
-                    for (let a = 0; a &lt; this.length; ++a) {
-                        var ind = utils.supercellIndex(a, [i, j, k], this._supercell,
-                            this.length);
-                        var aimg = this._atom_images[ind];
-                        // Is it in the box?
-                        var isin = _.reduce(aimg.xyz, function(r, x, e) {
-                            return (r &amp;&amp; (xmin[e] &lt;= x) &amp;&amp; (x &lt;= xmax[e]));
-                        }, true);
-                        if (isin)
-                            found.push(ind);
-                    }
-                }
-            }
-        }
-        return found;
-    }
-    /**
-     * @private
-     */
-    _querySphere(x0, r) {
-        if (x0 instanceof AtomImage) {
-            x0 = x0.xyz; // Can use an atom as centre
-        }
-        var scell = [1, 1, 1];
-        var cell0 = [0, 0, 0];
-        var fx0 = this.absToFrac(x0);
-        if (this.periodic) {
-            // Supercell necessary for the search?
-            scell = this.minimumSupercell(r);
-            cell0 = _.map(fx0, Math.floor);
-        }
-        var fxmin;
-        var fxmax;
-        if (this.periodic) {
-            fxmin = _.zipWith(cell0, scell, function(c0, s) {
-                return c0 - (s - 1) / 2;
-            });
-            fxmax = _.zipWith(cell0, scell, function(c0, s) {
-                return c0 + (s + 1) / 2;
-            });
-            // Now add supercell limits
-            var scmin = this._supercell_grid[0];
-            var scmax = this._supercell_grid[this._supercell_grid.length - 1];
-            fxmin = _.zipWith(fxmin, scmin, function(f, s) {
-                return Math.max(f, s);
-            });
-            fxmax = _.zipWith(fxmax, scmax, function(f, s) {
-                return Math.min(f, s + 1);
-            });
-        } else {
-            fxmin = [0, 0, 0];
-            fxmax = [1, 1, 1];
-        }
-        var found = [];
-        for (let i = fxmin[0]; i &lt; fxmax[0]; ++i) {
-            for (let j = fxmin[1]; j &lt; fxmax[1]; ++j) {
-                for (let k = fxmin[2]; k &lt; fxmax[2]; ++k) {
-                    for (let a = 0; a &lt; this.length; ++a) {
-                        var ind = utils.supercellIndex(a, [i, j, k], this._supercell,
-                            this.length);
-                        var aimg = this._atom_images[ind];
-                        // Is it in the sphere?
-                        var isin = mjs.distance(aimg.xyz, x0) &lt;= r;
-                        if (isin)
-                            found.push(ind);
-                    }
-                }
-            }
-        }
-        return found;
-    }
-    /**
-     * @private
-     */
-    _queryBonded(atoms, distance = 1, exact = false) {
-        if (atoms instanceof AtomImage || typeof(atoms) == 'number') {
-            atoms = [atoms];
-        }
-        if (atoms instanceof ModelView) {
-            atoms = atoms._images;
-        }
-        if (atoms instanceof Array &amp;&amp; typeof(atoms[0]) == 'number') {
-            var imgs = this._atom_images;
-            atoms = _.map(atoms, function(i) {
-                return imgs[i];
-            });
-        }
-        if (distance &lt; 1) {
-            return [];
-        }
-        function a2ii(a) {
-            return a.imgIndex;
-        }
-        // Find all atoms that are at most [distance] bonds away from the ones
-        // passed as argument
-        var bonded_tree = [atoms]; // We start with distance zero and build up
-        var found = [];
-        for (let d = 1; d &lt;= distance; ++d) {
-            var previous = bonded_tree[d - 1];
-            var next = [];
-            for (let i = 0; i &lt; previous.length; ++i) {
-                next = next.concat(previous[i].bondedAtoms);
-            }
-            bonded_tree.push(next);
-            if (!exact) {
-                found = found.concat(_.map(next, a2ii));
-            } else if (d == distance) {
-                found = _.map(next, a2ii);
-            }
-        }
-        found = _.uniq(found); // Remove duplicate values
-        found = _.difference(found, _.map(bonded_tree[0], function(a) {
-            return a.imgIndex;
-        })); // Remove the starting atoms
-        return found;
-    }
-    /**
-     * @private
-     */
-    _queryMolecule(atoms) {
-        if (atoms instanceof AtomImage || typeof(atoms) == 'number') {
-            atoms = [atoms];
-        }
-        if (atoms instanceof ModelView) {
-            atoms = atoms._images;
-        }
-        if (atoms instanceof Array &amp;&amp; typeof(atoms[0]) == 'number') {
-            var imgs = this._atom_images;
-            atoms = _.map(atoms, function(i) {
-                return imgs[i];
-            });
-        }
-        var found = [];
-        // For each atom, select the whole molecule
-        for (let i = 0; i &lt; atoms.length; ++atoms) {
-            var a = atoms[i];
-            var ind = a.index;
-            var mol_ind = this._molinds[ind];
-            var mol = this._molecules[mol_ind];
-            // Identify the atom
-            var c0 = _.find(mol, function(am) {
-                return am.index == ind;
-            }).cell;
-            // Supercell indices?
-            for (let j = 0; j &lt; mol.length; ++j) {
-                var am = mol[j];
-                var cm = mjs.subtract(am.cell, c0);
-                var im = am.index;
-                var iim = utils.supercellIndex(im, cm, this._supercell, this.length);
-                if (iim >= 0 &amp;&amp; iim &lt; this._atom_images.length) {
-                    found.push(iim);
-                }
-            }
-        }
-        return found;
-    }
-}
-export {
-    AtomImage,
-    BondImage,
-    Model
-}</code></pre></article></section></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div class="wrapper" id="iCxFxjkHbP"><button class="icon-button search-close-button" id="VjLlGakifb" aria-label="close search"><svg><use xlink:href="#close-icon"></use></svg></button><div class="search-box-c"><svg><use xlink:href="#search-icon"></use></svg> <input type="text" id="vpcKVYIppa" class="search-input" placeholder="Search..." autofocus></div><div class="search-result-c" id="fWwVHRuDuN"><span class="search-result-c-text">Type anything to view search result</span></div></div></div><div class="mobile-menu-icon-container"><button class="icon-button" id="mobile-menu" data-isopen="false" aria-label="menu"><svg><use xlink:href="#menu-icon"></use></svg></button></div><div id="mobile-sidebar" class="mobile-sidebar-container"><div class="mobile-sidebar-wrapper"><div class="mobile-nav-links"></div><div class="mobile-sidebar-items-c"><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-modules"><div>Modules</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js.html">lib/model.js</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js.html">lib/modelview.js</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-classes"><div>Classes</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div><div class="mobile-navbar-actions"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div></div></div><script type="text/javascript" src="scripts/core.min.js"></script><script src="scripts/search.min.js" defer="defer"></script><script src="scripts/third-party/fuse.js" defer="defer"></script><script type="text/javascript">var tocbotInstance=tocbot.init({tocSelector:"#eed4d2a0bfd64539bb9df78095dec881",contentSelector:".main-content",headingSelector:"h1, h2, h3",hasInnerContainers:!0,scrollContainer:".main-content",headingsOffset:130,onClick:bringLinkToView})</script></body></html>